Study characteristics

Figure S1. Data coverage by geography

Number of observations in the primary dataset at each administrative level by country. Countries with >10 observations displayed as 10.


Figure S2. Data coverage over time

Number of observations in the primary dataset within different time periods. Year represents the year sampling was completed. Excludes 9 observations missing a study end date.


Table 1. Study characteristics

Number of observations with each study characteristic.

variable value Total Percent
Study design Diagnostic test accuracy 28 21.2
Study design Other 1 0.8
Study design Surveillance 93 70.5
Study design Vaccine effectiveness 10 7.6
Sampling quality High 37 28.0
Sampling quality Low 95 72.0
Prop lab tested 0-5 12 9.1
Prop lab tested 5-50 32 24.2
Prop lab tested 50-95 27 20.5
Prop lab tested 95+ 30 22.7
Prop lab tested Not reported 31 23.5
Num tests 1 106 80.3
Num tests 2 19 14.4
Num tests 3+ 7 5.3
N 1-9 1 0.8
N 10-99 37 28.0
N 100-999 55 41.7
N 1000+ 39 29.5


Table S2. Characteristics of suspected cholera cases reported by each study

variable value Total Percent
Prop vaccinated No 127 96.2
Prop vaccinated Yes 5 3.8
Prop severe dehyd No 121 91.7
Prop severe dehyd Yes 11 8.3
Prop mod dehyd No 123 93.2
Prop mod dehyd Yes 9 6.8
Prop female No 104 78.8
Prop female Yes 28 21.2
Prop antibiotics No 122 92.4
Prop antibiotics Yes 10 7.6
Prop 5 and severe dehyd No 126 95.5
Prop 5 and severe dehyd Yes 6 4.5
Prop 5 and dehyd and antibiotics No 131 99.2
Prop 5 and dehyd and antibiotics Yes 1 0.8
Prop 5 No 100 75.8
Prop 5 Yes 32 24.2
Prop 15 No 114 86.4
Prop 15 Yes 18 13.6


V. cholerae positivity in unadjusted data

Figure 2. Vibrio cholerae positivity by study methodology and outbreak context

Proportion of suspected cholera cases that were confirmed positive by A) diagnostic test type, B) quality of sampling methods, where “high” includes all suspected cases or a random or stratified sample and “low” includes convenience or unreported sampling methods, C) age minimum in suspected case definition, where “0” indicates that no minimum age was set, and D) whether surveillance was initiated in response to an outbreak or whether it was routine surveillance or non-outbreak. Each point is an observation. Boxes represent the mean and interquartile range of positivity for each group. Lines extend from the top and bottom of box to the largest positivity value no further than 1.5 * IQR from the box.


Figure S3. Vibrio cholerae positivity by incidence and suspected case characteristics

Relationship between reported V. cholerae positivity and A) proportion of suspected cholera cases tests that were under 5 years of age, B) suspected cholera incidence rate per 10,000 at study site, C) proportion of suspected cases severely dehydrated, and D) proportion of suspected cases on antibiotics prior to testing. Size of the points is proportional to the number of cases tested, and shapes indicate which diagnostic test was used to confirm V. cholerae infection. Confidence intervals for Spearman rank correlation coefficients estimated using bootstrapping (nrep=1000). Smoothing method is loess (without weights). In B) estimated suspected cholera incidence rates for 2010-2016 (Lessler et al., 2018) were aggregated to the administrative division that best represented each study’s catchment area by dividing the total estimated cholera cases in each area by its estimated population.


Adjusted underlying V. cholerae positivity

Table S3. Estimated sensitivity and specificity of each diagnostic test

Estimate is median sensitivity and specificity pooled across four studies that reported results for all diagnostics tests, as described in Methods. Parentheses show 95% Credible Interval.

Measure Test Estimate (%)
Sensitivity Culture 82 ( 37.5 - 98.7 )
Sensitivity PCR 85.1 ( 53.6 - 98.9 )
Sensitivity RDT 90.4 ( 55.2 - 99.5 )
Specificity Culture 94.3 ( 81.5 - 99.6 )
Specificity PCR 94.2 ( 81.1 - 99.7 )
Specificity RDT 88.9 ( 54.8 - 99.4 )


Figure S4. Posterior distributions of V. cholerae positivity

Posterior distributions of V. cholerae positivity estimated using the random-effects model corresponding to results in Table S4. A) Unadjusted. B) Adjusted for test performance. C) Adjusted for test performance, sensitivity analysis shifting prior on alpha from Normal(0,2) as in A-B to Normal(0.9,2). On the left, prior (green) and posterior distribution (purple) of the global intercept are shown in logit space. On the right, histograms of estimated V. cholerae positivity.


Table S4. Estimated underlying V. cholerae O1/O139 positivity

“Unadjusted” is mean V. cholerae positivity (95% credible interval) from random effects meta-analysis without adjustments for test performance. “Adjusted” refers to V. cholerae estimates additionally adjusted for test performance, where the primary analysis includes a Normal(0,2) prior on the global intercept and a sensitivity analysis includes the prior shifted to Normal(0.9,2). “Stratified estimate for high quality…” corresponds to post-stratified estimates of V. cholerae positivity for studies that use high quality sampling methods and whether an age minimum was set in the suspected case definition, as well as whether surveillance was initiated in response to an outbreak.

Version Positivity (%)
Unadjusted 46.4 ( 7.7 - 89.2 )
Adjusted for test performance 52.2 ( 24.2 - 79.8 )
Adjusted for test performance, prior on alpha shifted 54.8 ( 21 - 85.3 )
Stratified estimate for high quality sample with no known age restriction 45.9 ( 18.8 - 75.5 )
Stratified estimate for high quality sample with any age restriction 68.2 ( 32.6 - 97.6 )
Stratified estimate for high quality sample during non-outbreak surveillance 41.7 ( 11.9 - 77 )
Stratified estimate for high quality sample during outbreak surveillance 78.2 ( 39.7 - 99.1 )


Figure 3. Estimated underlying V. cholerae positivity

A) Posterior distributions of pooled percent sensitivity and specificity of culture (top), PCR (middle), and RDT (bottom) for detecting V. cholerae O1O139 infections in suspected cholera cases. Dashed lines represent mean values of each distribution. B) “Unadjusted” is mean V. cholerae positivity (95% credible interval) from random effects meta-analysis without adjustments for test performance. “Adjusted for test performance” is estimated mean V. cholerae positivity (95% credible interval), adjusted for sensitivity/specificity of the tests. High-quality stratified estimates corresponds to post-stratified estimates of V. cholerae positivity for studies that use high quality sampling methods and whether an age minimum was set in the suspected case definition, as well as whether surveillance was initiated in response to an outbreak.


Figure 4. Forest plot of study estimates and underlying positivity

Black points indicate mean study-level underlying positivity and 95% Credible Interval (CI). Teal, orange, and purple points indicate the proportion positive reported by study for culture, PCR, and RDT, respectively, and corresponding error bars indicate 95% confidence interval for a binomial probability, estimated with the normal approximation. Studies are labeled by country ISO3 code, whether they used high quality sampling methods, and whether a minimum age was set in the suspected cholera case definition. Studies are split into outbreak and non-outbreak for ease of interpretation.

## I2: 99.99675, 99.99681, 99.99687, ; tau2: 0.9419, 0.96145, 0.97747,


Factors associated with variation in V. cholerae positivity

Table S5. Odds of V. cholerae positivity by age and outbreak context

Odds that a suspected cholera case seeking testing or care has a true V. cholerae O1/O139 infection with low sampling quality compared to high sampling quality, with any minimum age set in suspected case definition, and with surveillance initiated in response to an outbreak compared to non-outbreak surveillance (i.e., routine or post-vaccination surveillance).

Variable Odds ratio
Low sampling quality 3.8 ( 0.95 - 9.86 )
Minimum age in case definition 2.33 ( 0.54 - 6.4 )
Outbreak surveillance 5.71 ( 1.53 - 15.43 )